The identification of candidate radio marker genes using a coexpression network analysis in gamma‐irradiated rice

Plant physiological and biochemical processes are significantly affected by gamma irradiation stress. In addition, gamma‐ray (GA) differentially affects gene expression across the whole genome. In this study, we identified radio marker genes (RMGs) responding only to GA stress compared with six abiotic stresses (chilling, cold, anoxia, heat, drought and salt) in rice. To analyze the expression patterns of differentially expressed genes (DEGs) in gamma‐irradiated rice plants against six abiotic stresses, we conducted a hierarchical clustering analysis by using a complete linkage algorithm. The up‐ and downregulated DEGs were observed against six abiotic stresses in three and four clusters among a total of 31 clusters, respectively. The common gene ontology functions of upregulated DEGs in clusters 9 and 19 are associated with oxidative stress. In a Pearson's correlation coefficient analysis, GA stress showed highly negative correlation with salt stress. On the basis of specific data about the upregulated DEGs, we identified the 40 candidate RMGs that are induced by gamma irradiation. These candidate RMGs, except two genes, were more highly induced in rice roots than in other tissues. In addition, we obtained other 38 root‐induced genes by using a coexpression network analysis of the specific upregulated candidate RMGs in an ARACNE algorithm. Among these genes, we selected 16 RMGs and 11 genes coexpressed with three RMGs to validate coexpression network results. RT‐PCR assay confirmed that these genes were highly upregulated in GA treatment. All 76 genes (38 root‐induced genes and 38 candidate RMGs) might be useful for the detection of GA sensitivity in rice roots.     

东乡野生稻苗期响应低温胁迫的转录组分析

为了解东乡野生稻（Oryza rufipogon）对低温胁迫的响应机制,对苗期的RNA-seq转录表达谱进行了研究。结果表明,与对照相比,共检测到10 200个差异表达基因（DEGs）,其中5 201个上调表达,4 999个下调表达,其中有426个DEGs位于已报道的水稻耐冷QTL区间,且37个为耐冷调控相关的家族基因。GO功能分类和KEGG代谢路径分析表明,核酸结合转录因子活性、氨基酸生物合成以及光合作用代谢等均参与响应低温胁迫过程。实时荧光定量分析表明,ABA响应蛋白基因、MYB转录因子和40S核糖体蛋白SA基因等12个可能与低温胁迫响应相关的DEGs表达模式与RNA-seq的一致。可见,植物激素传导途径和转录因子相关调控基因在东乡野生稻苗期响应低温胁迫过程中起重要作用。     

Differential expression of cell wall related genes in the elongation zone of rice roots under water deficit

Growth in the apical elongation zone of plant roots is central to the development of functional root systems. It has been known that rice seminal root elongation could be enhanced by water stress. In the present study, 17 cell-wall related genes were identified by cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique. Five genes encoded cell-wall loosening enzymes and six genes were involved in the lignin biosynthesis. The six other genes were related to the metabolism of polysaccharide and protein matrices in cell wall. Northern blot analysis confirmed that they were differentially expressed in the elongation zone of rice seminal roots under water stress, and none of them was root-specific. The results indicated that the activity of cell-wall loosening enzymes was enhanced in the early stage (within 16 h), and some cell wall matrices were synthesized rapidly in the middle stages (from 16 to 48 h), while lignin biosynthesis was enhanced in the middle and late stages of water stress (from 48 to 72 h). Published in Russian in Fiziologiya Rastenii, 2006, Vol. 53, No. 3, pp. 437–443. The text was submitted by the authors in English.     

Gene expression profiles in rice roots under low phosphorus stress

Phosphorus (P), an important plant macronutrient, is a component of key molecules such as nucleic acids, phospholipids and ATP. P is often the limiting nutrient for crop yield potential because of the low concentration of soluble P that can be absorbed directly by plant. Plants have evolved a series of molecular and morphological adaptations to cope with P limitation. However, the molecular bases of these responses to P deficiency have not been thoroughly elucidated. In this report, the gene expression profiles of low-P-tolerant rice Zhongzao 18 (Oryza sativa ssp. Indica) and not-low-P-tolerant rice Lagrue (Oryza sativa ssp. Indica) roots at 6 h, 24 h and 72 h under low P stress were investigated and compared with a control (normal P conditions) profile, using a DNA chip of 60,000 oligos (70 mer) that represented all putative genes of the rice genome. A total of 1,518 and 2,358 genes exhibited alterations in expression in response to low P stress in at least one of the three time points in rice Zhongzao 18 and rice Lagrue, respectively. The differentially expressed genes included those involved in phosphate (Pi) transportation, transportations except for Pi transportation, phosphatase, enzymes other than phosphatase, primary metabolism, secondary metabolism and so on. Several genes involved in glycolysis and TCA cycle were up-regulated during the early stages of low P treatment in rice Zhongzao 18 roots, but not in rice Lagrue roots. The results may provide useful information to further studies of the molecular mechanism of plant adaptation to low P and thus facilitate research in improving P utilization in crop species.     

Salt tolerance in crop plants: new approaches through tissue culture and gene regulation

Recent approaches to study of salinity tolerance in crop plants have ranged from genetic mapping to molecular characterization of gene products induced by salt/drought stress. Transgenic plant design has allowed to test the effects of overexpression of specific prokaryotic or plant genes that are known to be up-regulated by salt/drought stress. This review summarizes current progress in the field in the context of adaptive metabolic and physiological responses to salt stress and their potential role in long term tolerance. Specifically considered are gene activation by salt, in view of proposed avenues for improved salt tolerance and the need to ascertain the additional influences of developmental regulation of such genes. Discussion includes the alternate genetic strategy we have pursued for improving salinity tolerance in alfalfa (Medicago sativa L.) and rice (Oryza sativa L.). This strategy combines single-step selection of salt-tolerant cells in culture, followed by regeneration of salt-tolerant plants and identification of genes important in conferring salt tolerance. We have postulated that activation or improved expression of a subset of genes encoding functions that are particularly vulnerable under conditions of salt-stress could counteract the molecular effects of such stress and could provide incremental improvements in tolerance. We have proceeded to identify the acquired specific changes in gene regulation for our salt-tolerant mutant cells and plants. One particularly interesting and novel gene isolate from the salt-tolerant cells is Alfin1, which encodes a putative zinc-finger regulatory protein, expressed predominantly in roots. We have demonstrated that this protein binds DNA in a sequence specific manner and may be potentially important in gene regulation in roots in response to salt and an important marker for salt tolerance in crop plants.     

Salt tolerance of barley: Relations between expression of isoforms of vacuolar Na<Superscript>+</Superscript>/H<Superscript>+</Superscript>-antiporter and <Superscript>22</Superscript>Na<Superscript>+</Superscript> accumulation

Two barley cultivars (Hordeum vulgare L., cvs. Elo and Belogorskii) differing in salt tolerance were used to study ²²Na⁺ uptake, expression of three isoforms of the Na⁺/H⁺ antiporter HvNHX1-3, and the cellular localization of these isoforms in the elongation zone of seedling roots. During short (1 h) incubation, seedling roots of both cultivars accumulated approximately equal quantities of ²²Na⁺. However, after 24-h incubation the content of ²²Na⁺ in roots of a salt-tolerant variety Elo was 40% lower than in roots of the susceptible variety Belogorskii. The content of ²²Na⁺ accumulated in shoots of cv. Elo after 24-h incubation was 6.5 times lower than in shoots of cv. Belogorskii and it was 4 times lower after the salt stress treatment. The cytochemical examination revealed that three proteins HvNHX1-3 are co-localized in the same cells of almost all root tissues; these proteins were present in the tonoplast and prevacuolar vesicles. Western blot analysis of HvNHX1-3 has shown that the content of isoforms in vacuolar membranes increased in response to salt stress in seedling roots and shoots of both cultivars, although the increase was more pronounced in the tolerant cultivar. The content of HvNHX1 in the seedlings increased in parallel with the enhanced expression of HvNHX1, whereas the increase in HvNHX2 and HvNHX3 protein content was accompanied by only slight changes in expression of respective genes. The results provide evidence that salt tolerance of barley depends on plant ability to restrict Na⁺ transport from the root to the shoot and relies on regulatory pathways of HvNHX1-3 expression in roots and shoots during salt stress.